return cigar; if ( numIndels == 1 ) return leftAlignSingleIndel(cigar, refSeq, readSeq, refIndex, readIndex, true);
if (ce.getOperator() == CigarOperator.D || ce.getOperator() == CigarOperator.I) { cigarToAlign.add(ce); final Cigar leftAligned = AlignmentUtils.leftAlignSingleIndel(cigarToAlign, refSeq, readSeq, refIndex, readIndex, false); for ( final CigarElement toAdd : leftAligned.getCigarElements() ) { cigarToReturn.add(toAdd); } refIndex += cigarToAlign.getReferenceLength();